Physics of coral reef systems in a shallow tidal embayment

Ongoing deforestation in the tropics involves higher river discharges and an increase of runoff, which has consequences to coastal ecosystems. The dispersal of fluvial sediment and freshwater by marine processes affects the environmental determinants of coral reefs near the coast, which include temperature, salinity, light and nutrient concentration. The central objective of this thesis is to identify the physical mechanisms that govern (1) the regional variability of vertical mixing, salinity, turbidity, and the supply of terrestrial sediment in coastal reef environments and (2) the local sedimentary processes at reef slopes, determining turbidity and sedimentation. The object of study was the Bay of Banten, which represents a shallow coastal embayment where coral reefs are subject to relatively turbid marine conditions. Field data were gathered within the framework of the Teluk Banten Research Programme, which is an Indonesian-Dutch research programme focussing on the social-economy, biology, geology and physical oceanography of to the Bay of Banten, Indonesia. The Teluk Banten Research Program is part of the Global Change Program of the Royal Netherlands Academy of Sciences (KNAW), and coordinated by the Foundation for the Advancement of Tropical Research (WOTRO). The study revealed that the key issues determining the delicate subsistence of shallow-water reefs in the Bay of Banten include mixing in the freshwater source region, the seasonal coupling between coastal processes and local resuspension of sediment. The topography-controlled mixing of small river discharges with the ambient marine waters inhibits the direct exposure of coral reefs to river-derived sediment suspensions, high nutrient loads and low salinity. The reefs near the coast benefit from relatively strong currents in front of an abandoned delta, which hydrodynamically acts like a coastal headland. Due to a seasonal coupling between river discharge, wind-driven throughflow and wave attack on the eroding delta, coral reefs in the Bay of Banten are protected from prolonged inundation by high-turbidity water masses that originate from the eroding delta. Local currents that induce resuspension of sediment at the reef slopes are the main control on turbidity variation in the waters that surround the coral reefs. Sediment that is already available may be resuspended and deposited repeatedly, which limits the role of regional advection of sediment. Backscatter data from an Acoustic Doppler Current Profiler (ADCP) have provided a valuable measure of suspended sediment concentration, revealing the spatial structure of sediment clouds connected to the reefs. The analysis of tides in the Bay of Banten gave cause for a general study on the asymmetry of sediment transport in mixed diurnal ? semidiurnal tidal regimes. In these regimes, tidal asymmetry is not only caused by nonlinear tidal interaction, but is also generated by astronomical tides in absence of shallow-water effects. In particular, the K1, O-1 and M2 constituents give an asymmetrical periodic flow pattern, with the largest peak velocities persistently in the same direction. A theoretical explanation for this phenomenon has been presented, and an inventory has been made of other, subordinate constituents that may contribute to repetitive asymmetric flow patterns. Analytical expressions have been derived which quantify the residual transport of sediment due to the K1, O-1 and M2 tides, as a function of the phases and amplitudes of these constituents, and the time lag between variation in suspended sediment transport and flow velocity